| Cancer | Cardiovascular disease | Digestive System Disorder | Immune System Disorder | Metabolic Disorder | Neurological Disorder | Other Disease | Total |
|---|---|---|---|---|---|---|---|
| 66 | 51 | 75 | 74 | 18 | 162 | 105 | 477 |
CRITICAL NOTE ON THESE PLOTS:
Unfortunately these plots were not able to be configured as I desired. For unknown reasons the row order was not able to be changed, and due to time constraints I wasn’t able to resolve this issue before generating the plots. Further the GBR sub population within the “mean-allele-frequency” bar graphs is evidently incorrect. Some error in preprocessing occurred with this sub population which can be seen in these graphs, thus the GBR population comparison here should be ignored.
NOTE: All tables will be displayed partially here and can be downloaded for complete viewing from the “tables_(csv)” folder
| VariantID | MAPPED_GENE | EnsVar_most_severe_consequence | DISEASE/TRAIT | MAPPED_TRAIT | Parent term | population_labels | Fst_per_population |
|---|---|---|---|---|---|---|---|
| rs10032909 | LINC01088 | intron_variant | Systemic lupus erythematosus | obsolete_systemic lupus erythematosus | Immune system disorder | EUR | 0.3539 |
| rs10035291 | SSBP2 | intron_variant | Bipolar disorder | obsolete_bipolar disorder | Neurological disorder | LWK | 0.5033 |
| rs1012621 | TGM3 | intron_variant | Inflammatory skin disease | atopic eczema, psoriasis | Other disease | ASW | 0.3138 |
| rs1012621 | TGM3 | intron_variant | Inflammatory skin disease | atopic eczema, psoriasis | Immune system disorder | ASW | 0.3138 |
| rs1016189 | MAGI2 | intron_variant | Acute graft-versus-host disease (gut) (recipient effect) | acute graft vs. host disease | Immune system disorder | FIN | 0.3603 |
| rs10245867 | JAZF1 | intron_variant | Multiple sclerosis | multiple sclerosis | Immune system disorder | CHS | 0.4332 |
| VariantID | MAPPED_GENE | EnsVar_most_severe_consequence | DISEASE/TRAIT | MAPPED_TRAIT | Parent term | population_labels_mono | Fst_per_population |
|---|---|---|---|---|---|---|---|
| rs10031265 | PKD2 | intron_variant | Serum creatinine levels | creatinine measurement | Other measurement | CEU|CLM|ESN|GBR | 0.2316|0.1771|0.3568|0.2268 |
| rs10151945 | ATXN3 | 3_prime_UTR_variant | Lung function (FVC) | vital capacity | Other measurement | AMR|PEL | 0.1065|0.3051 |
| rs10154834 | GLB1 | intron_variant | Medication use (glucocorticoids) | Glucocorticoid use measurement | Other measurement | CLM|ITU | 0.2468|0.192 |
| rs10533065 | CASR | intron_variant | Eosinophil counts | eosinophil count | Hematological measurement | ASW | 0.2245 |
| rs10744953 | FBN1 | intron_variant | Ascending aorta minimum area | aortic measurement | Cardiovascular measurement | EUR|PJL|PUR | 0.2747|0.1734|0.1734 |
| rs10744953 | FBN1 | intron_variant | Ascending aorta minimum area | aortic measurement | Cardiovascular measurement | EUR|PJL|PUR | 0.2747|0.1734|0.1734 |
| VariantID | DISEASE/TRAIT | MAPPED_GENE | CONTEXT | INTERGENIC | RISK ALLELE FREQUENCY | MAPPED_TRAIT | EnsVar_most_severe_consequence | Parent term | monogenic_searched_resource | monogenic_disease_name |
|---|---|---|---|---|---|---|---|---|---|---|
| rs1078793 | Age at loss of ambulation in Duchenne muscular dystrophy | NA - RAMP3 | regulatory_region_variant | 1 | NR | Duchenne muscular dystrophy, disease progression measurement | regulatory_region_variant | Cardiovascular disease | A. Nesterova, Monogenic rare diseases in biomedical databases and text mining | SEE DISEASE/TRAIT |
| rs1078793 | Age at loss of ambulation in Duchenne muscular dystrophy | NA - RAMP3 | regulatory_region_variant | 1 | NR | Duchenne muscular dystrophy, disease progression measurement | regulatory_region_variant | Other measurement | A. Nesterova, Monogenic rare diseases in biomedical databases and text mining | SEE DISEASE/TRAIT |
| rs11017928 | Age at loss of ambulation in Duchenne muscular dystrophy | DOCK1 | intron_variant | 0 | NR | Duchenne muscular dystrophy, disease progression measurement | intron_variant | Cardiovascular disease | A. Nesterova, Monogenic rare diseases in biomedical databases and text mining | SEE DISEASE/TRAIT |
| rs11017928 | Age at loss of ambulation in Duchenne muscular dystrophy | DOCK1 | intron_variant | 0 | NR | Duchenne muscular dystrophy, disease progression measurement | intron_variant | Other measurement | A. Nesterova, Monogenic rare diseases in biomedical databases and text mining | SEE DISEASE/TRAIT |
| rs11641605 | Age at loss of ambulation in Duchenne muscular dystrophy | LINC02141 | intron_variant | 0 | NR | Duchenne muscular dystrophy, disease progression measurement | intron_variant | Cardiovascular disease | A. Nesterova, Monogenic rare diseases in biomedical databases and text mining | SEE DISEASE/TRAIT |
| rs11641605 | Age at loss of ambulation in Duchenne muscular dystrophy | LINC02141 | intron_variant | 0 | NR | Duchenne muscular dystrophy, disease progression measurement | intron_variant | Other measurement | A. Nesterova, Monogenic rare diseases in biomedical databases and text mining | SEE DISEASE/TRAIT |
platform x86_64-w64-mingw32
arch x86_64
os mingw32
crt ucrt
system x86_64, mingw32
status
major 4
minor 2.1
year 2022
month 06
day 23
svn rev 82513
language R
version.string R version 4.2.1 (2022-06-23 ucrt) nickname Funny-Looking
Kid
Package Version
curl 4.3.2
data.table 1.14.2
dplyr 1.0.10
esquisse 1.1.2
ggplot2 3.3.6
ggrepel 0.9.3
httr 1.4.4
jsonlite 1.8.0
knitr 1.40
purrr 0.3.4
tibble 3.1.8
tidyr 1.2.1
GWASpops.pheno2geno 0.900